Variant report

Variant	rs61473560
Chromosome Location	chr1:175532859-175532860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175528817..175531396-chr1:175532065..175533684,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNN-3	chr1:175531373-175533005	NONHSAT007757

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10158732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913005	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10913006	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10913010	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913012	0.92[ASN][1000 genomes]
rs10913013	0.90[ASN][1000 genomes]
rs10913014	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12077972	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565044	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565695	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848622	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848658	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16848698	0.83[AMR][1000 genomes]
rs16848703	0.83[AMR][1000 genomes]
rs2205832	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2205833	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2205834	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57107679	0.80[AMR][1000 genomes]
rs58376805	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59377605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61299618	0.80[AMR][1000 genomes]
rs6657672	0.92[ASN][1000 genomes]
rs6691558	0.90[ASN][1000 genomes]
rs6693340	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6693370	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6700514	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703015	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7354864	0.85[ASN][1000 genomes]
rs7514520	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516879	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9286909	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999586	chr1:175428957-175765789	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1014015	chr1:175430199-175752187	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1012012	chr1:175430199-175760752	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1000135	chr1:175430199-175765789	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1008727	chr1:175430808-175752725	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1008620	chr1:175430808-175760752	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv527256	chr1:175430855-175582250	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv466072	chr1:175430855-175739003	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv548243	chr1:175430855-175739003	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv528975	chr1:175430855-175757242	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv466083	chr1:175430855-175757242	Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv548244	chr1:175430855-175757242	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv548245	chr1:175430855-175772378	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1004585	chr1:175436519-175739951	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv998119	chr1:175436519-175760752	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv948460	chr1:175439176-175751385	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1011962	chr1:175440153-175760752	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	esv33328	chr1:175446583-175910001	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv915955	chr1:175448830-175704923	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv998327	chr1:175448846-175704803	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv535211	chr1:175448846-175704803	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1001391	chr1:175448870-175728998	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv535212	chr1:175448870-175728998	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv508659	chr1:175495780-175547908	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175518400-175537600	Weak transcription	Pancreas	Pancrea
2	chr1:175531600-175534600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:175531600-175534800	Enhancers	Fetal Stomach	stomach
4	chr1:175531800-175534800	Enhancers	Fetal Muscle Leg	muscle
5	chr1:175532000-175533400	Bivalent Enhancer	Fetal Heart	heart
6	chr1:175532000-175534200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:175532000-175534800	Enhancers	Fetal Brain Male	brain
8	chr1:175532200-175533200	Enhancers	Brain Anterior Caudate	brain
9	chr1:175532200-175533200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:175532200-175534000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:175532400-175533400	Enhancers	Brain Angular Gyrus	brain
12	chr1:175532400-175533400	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:175532400-175533600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:175532400-175533600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:175532400-175534000	Enhancers	Fetal Lung	lung
16	chr1:175532400-175534200	Enhancers	Brain Hippocampus Middle	brain
17	chr1:175532400-175534200	Enhancers	Brain Substantia Nigra	brain
18	chr1:175532600-175533000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
19	chr1:175532600-175533000	Enhancers	Colon Smooth Muscle	Colon
20	chr1:175532600-175533600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:175532600-175534000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:175532600-175534200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr1:175532600-175534200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:175532600-175534400	Enhancers	H9 Cell Line	embryonic stem cell
25	chr1:175532600-175534600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
26	chr1:175532600-175534600	Enhancers	Brain Germinal Matrix	brain
27	chr1:175532800-175533000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
28	chr1:175532800-175533000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr1:175532800-175533200	Flanking Active TSS	Fetal Brain Female	brain
30	chr1:175532800-175533800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:175532800-175534600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:175532800-175535600	Enhancers	Fetal Intestine Large	intestine

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